This report assesses the PPA Bibliography in regards to different measures and shows some information of the content. It does not assess the content of the sources but rather the bibliometric data.
Cleanliness of a bibliography is defined here as the quality of the bibliografic data in the bibliography. It does not concern any topical measures, only measures related to the bibliografic data in the bibliography.
The analysis is at the moment only done for DOIs as corresponding measures are not available at the moment for ISBNs and ISSNs and duplicate ISBNs and ISSNs can be rcorrect as div=fferent chapters of a book might be in the bibliography.
To identify a reference, the most widely used identifier is the DOI. The following table shows the number of references with a DOI and the number of unique DOIs.
To consider duplicate ISBNs or ISSNs as duplicates entries in the library is not waranted as e.g. differenc chapters of a book can be separate entries in the library and therefore lead to duplicates.
The foilowing sections provide some more detailed analysis of the bibliography in Zenodo. The tables all contain clickable links which, shwen clicked, show the respective article in the Zotero bibliograpohy.
The following DOIs are duplicates in the bibliography. This table should be empty.
if (length(bib_data$metrics$zotero_dois$duplicate) > 0) {
data.frame(
doi = bib_data$metrics$zotero_dois$duplicate,
link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$duplicate))
) |>
dplyr::mutate(
doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
link = NULL
) |>
knitr::kable(
caption = "DOIs in Zenodo which are duplicated",
escape = FALSE
)
}All DOIs should be given as only the DOI without the resolver, i.e. not starting withhttp`. The following table shows all entries which do have a non-copnform DOI:
#|
http <- grep("http", bib_data$metrics$zotero_dois$id_raw)
data.frame(
doi = bib_data$metrics$zotero_dois$id_raw[http],
link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$id_raw)[http])
) |>
dplyr::mutate(
doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
link = NULL
) |>
knitr::kable(
caption = "DOIs in Zenodo which include a `http`",
escape = FALSE
)| doi | |
|---|---|
| HS3NDPZ8 | https://doi.org/10.1890/1540-9295(2007)5[80:SHIUER]2.0.CO;2 |
| 4ZI4KS98 | http://dx.doi.org/10.5751/ |
| NQSUD2SH | http://dx.doi.org/10.1371/journal.pone.0094459 |
Here we do acheck for the structural validity of the dois. This check needs to be improved. Of these 52 are not valid. These are:
#|
data.frame(
doi = bib_data$metrics$zotero_dois$not_valid,
link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$not_valid))
) |>
dplyr::mutate(
doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
link = NULL
) |>
knitr::kable(
caption = "DOIs in Zenodo which ar not valid",
escape = FALSE
)| doi | |
|---|---|
| Y5NSPPUH | e0118748 |
| ALGHGTVC | 10. 1111/1462-2920.12426 |
| UTY8BT2Z | 10.1641/0006-3568(2001)051[0625:RHOREM]2.0.CO;2 |
| NCX3RHJN | e111629 |
| HS3NDPZ8 | 10.1890/1540-9295(2007)5[80:SHIUER]2.0.CO;2 |
| 4ZI4KS98 | 10.5751/ |
| I3LT26P2 | 10.2984/1534-6188(2007)61[173:csoteb]2.0.co;2 |
| QA7ES7M2 | 10.1603/0013-8746(2000)093[0415:mdriae]2.0.co;2 |
| AYNKG7GY | e1004816 |
| UH9IEFBP | 10.1674/0003-0031(2007)157[92:ropact]2.0.co;2 |
| P244RZKW | 10.1603/0013-8746(2001)094[0545:sypfot]2.0.co;2 |
| PYY5358N | 10.1603/0013-8746(2002)095[0345:cpeabh]2.0.co;2 |
| 8FC7HMHK | 10.1890/1051-0761(2000)010[0689:BICEGC]2.0.CO;2 |
To validate the existence and validity of the DOIs, we check if the DOIs are in the OpenAlex database.
Of the 996 unique DOIs in the library, 52 (5.22%) are in not in OpenAlex. This includes the non-valid DOIS, whci are filtered out in the table below.
data.frame(
doi = bib_data$metrics$zotero_dois$not_in_oa,
link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$not_in_oa))
) |>
dplyr::mutate(
doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
link = NULL
) |>
knitr::kable(
caption = "DOIs in Zenodo which ar not in [OpenAlex](https://OpenAlex.org){target='_blank'}",
escape = FALSE
)TODO Finally we check, if these dois exist but are not ingested into OpanAlex. This is done using the doi.org resolver This is disabled at the moment and still needs o=to be implemented.
In the bibliographic analysis, we can only analyse the references in OpenAlex as the bibliographic metadata alanised is not in the Zotero liubrary but retrieved from OpenAlex.
Works on Zenodo as well as on OpenAlex are of different types. Here we show these separate.
bib_data$figure_types_data |>
dplyr::arrange(
from,
desc(count)
) |>
knitr::kable(
caption = "Types of documents from the Zotero bibliography as well as from OpenApex."
)| type | count | from |
|---|---|---|
| article | 833 | OpenAlex |
| review | 103 | OpenAlex |
| book-chapter | 17 | OpenAlex |
| letter | 9 | OpenAlex |
| book | 6 | OpenAlex |
| preprint | 4 | OpenAlex |
| other | 2 | OpenAlex |
| editorial | 1 | OpenAlex |
| erratum | 1 | OpenAlex |
| journalArticle | 1148 | Zotero |
| book | 39 | Zotero |
| manuscript | 20 | Zotero |
| bookSection | 15 | Zotero |
| conferencePaper | 9 | Zotero |
| report | 4 | Zotero |
| thesis | 3 | Zotero |
| artwork | 2 | Zotero |
| document | 2 | Zotero |
| webpage | 2 | Zotero |
bib_data$figure_types
The types entered in the Zenodo library and the types as retrieved from OpenAlex are not linked, therefore they can differ, This can indicate problems but not necessarily has to. These cases need to be carefully evaluated and here only a starting point is given.
NA in OpenAlex is likely caused by the doi not found in OpenAlex (not in there, not valid, non-standard DOI in Zenodo). NA in Zotero is linked to non-standard DOI entries (i.e. with http) whcih can therefore not be linked to OpenAlex data. If all DOIs are in standard format, there should be no NAs in this Table in the column Ferom Zenodo.
Improvements should be done after feedback.
bib_data$metrics$types$comparison |>
knitr::kable(
col.names = c("Type from Zenodo", "Type from [OpenAlex](https://OpenAlex.org){target='_blank'}", "count"),
caption = "Table giving the combination of types from Zenodo as well as [OpenAlex](https://OpenAlex.org){target='_blank'} and their frequency"
)| Type from Zenodo | Type from OpenAlex | count |
|---|---|---|
| journalArticle | article | 918 |
| journalArticle | NA | 207 |
| journalArticle | review | 124 |
| book | NA | 39 |
| NA | article | 30 |
| manuscript | NA | 20 |
| journalArticle | book-chapter | 16 |
| bookSection | NA | 15 |
| journalArticle | letter | 9 |
| conferencePaper | NA | 6 |
| journalArticle | book | 6 |
| report | NA | 4 |
| journalArticle | preprint | 4 |
| thesis | NA | 3 |
| conferencePaper | article | 3 |
| webpage | NA | 2 |
| journalArticle | other | 2 |
| artwork | NA | 2 |
| document | NA | 2 |
| NA | review | 2 |
| journalArticle | erratum | 1 |
| journalArticle | editorial | 1 |
| NA | book-chapter | 1 |
bib_data$figure_pub_yearWarning: Removed 1 row containing missing values or values outside the scale range
(`geom_col()`).
This is checked by using the OpenAlex retrieved works. Therefore it is li=mited to the works that are on OpenAlex. At the moment, only references with a DOI were retrieved from OpenAlex.
bib_data$figure_oa_status
Based on the data entered in the bibliography on Zenodo
bib_data$figure_top_journals
This table contains all Journals as specified in the Zotero database.
bib_data$figure_top_journals_data |>
IPBES.R::table_dt("cited_journals")In this section we will take a closer look at the countries from which ih the authors ot the publication come. THe data comes from OpenAlex and includes all authoirs without weighting.
#|
#| fig-height: 10
#| fig-width: 10
bib_data$figure_top_country_map
This plot only contains the countries with more than 10 references.
#|
#| fig-height: 10
#| fig-width: 10
bib_data$figure_top_country
This table contains all countries and the number of authorship.
bib_data$figure_top_country_data |>
IPBES.R::table_dt("top_countries")